Galilean Invariant Thermostat

From: Ismail, Mohd F. (
Date: Sun Apr 08 2012 - 18:26:38 CDT

If one uses a non-galilean invariant thermostat, does the velocities of the particles change randomly? How will it affect the diffusion coefficient?

Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019

From: [] on behalf of johan strumpfer []
Sent: Monday, March 19, 2012 11:28 AM
To: Wang Yi
Cc: raghav singh;
Subject: Re: namd-l: SMD under NPT ensemble


Namd can do this, but you should be careful of which thermostat you
use. The Langevin thermostat is not Galilean invariant, so you should
not use it when doing SMD. To get around this you should use the
Lowe-Andersen thermostat which is Galilean invariant. In practice I've
also found that NVT to give more reliable results than NPT.


Johan Strumpfer:
Ph.D. Candidate
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA

On Mon, Mar 19, 2012 at 11:20 AM, Wang Yi <> wrote:
> There are instructions on how to do SMD in NAMD, using either the
> configuration file or the latest ColVar technique.
> You can find them in the NAMD manual online.
> ___________________________
> Yi (Yves) Wang
> Duke University
> On 2012-3-19, at $B>e8a(B11:12, raghav singh wrote:
> Hello All,
> I wanted to know about SMD simulation using NPT ensemble...
> NAMD has this freedom or not... any suggested article would be off great
> help.
> Thank You all
> regrads
> Raghav

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